Mercurial > repos > dereeper > sniplay

comparison PedToFasta/pedToFasta.xml @ 10:c6640c49fd01 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 09:00:24 -0400
parents 98c37a5d67f4
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9:98c37a5d67f4 10:c6640c49fd01
1 <tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0"> 1 <tool id="sniplay_pedToFasta" name="Ped2Fasta" version="2.0.0">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name --> 3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Convert PED file to Fasta File </description> 4 <description> Convert PED file to Fasta File </description>
5 5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
32 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/> 32 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
33 </inputs> 33 </inputs>
34 34
35 <!-- [REQUIRED] Output files --> 35 <!-- [REQUIRED] Output files -->
36 <outputs> 36 <outputs>
37 <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" /> 37 <data name="fileout" format="fasta" label="${fileout_label}.fa" />
38 </outputs> 38 </outputs>
39 39
40 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 40 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
41 <tests> 41 <tests>
42 <!-- [HELP] Test files have to be in the ~/test-data directory --> 42 <!-- [HELP] Test files have to be in the ~/test-data directory -->
45 <output name="fileout" file="ped2fasta-result.fa" /> 45 <output name="fileout" file="ped2fasta-result.fa" />
46 </test> 46 </test>
47 </tests> 47 </tests>
48 48
49 <!-- [OPTIONAL] Help displayed in Galaxy --> 49 <!-- [OPTIONAL] Help displayed in Galaxy -->
50 <help> 50 <help><![CDATA[
51 51
52 .. class:: infomark 52 .. class:: infomark
53 53
54 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform 54 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
55 55
56 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). 56 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
57 57
58 .. class:: infomark 58 .. class:: infomark
59 59
60 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. 60 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
61 61
62 .. class:: infomark 62 .. class:: infomark
63 63
64 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr 64 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
65 65
66 --------------------------------------------------- 66 ---------------------------------------------------
67 67
68 ========= 68 =========
69 Ped2Fasta 69 Ped2Fasta
71 71
72 ----------- 72 -----------
73 Description 73 Description
74 ----------- 74 -----------
75 75
76 Convert PED file to Fasta File 76 | Convert PED file to Fasta File
77
78 -----------------
79 Workflow position
80 -----------------
81
82 **Upstream tool**
83
84 =============== ========================== =======
85 Name output file(s) format
86 =============== ========================== =======
87 VCFtools Filter VCF file VCF
88 =============== ========================== =======
89
90
91 **Downstream tool**
92
93 =========== ========================== =======
94 Name input file(s) format
95 =========== ========================== =======
96 Readseq Fasta alignment fasta
97 =========== ========================== =======
98
99 77
100 ---------- 78 ----------
101 Input file 79 Input file
102 ---------- 80 ----------
103 81
104 PED file 82 PED file
105 PED file usually from VCF tools 83 PED file usually from VCF tools
106 84
107 ---------- 85 ---------
108 Parameters 86 Parameter
109 ---------- 87 ---------
110 88
111 Output file name 89 Output file name
112 Prefix for the output fasta file 90 Prefix for the output fasta file
113 91
114 ------------ 92 -----------
115 Output files 93 Output file
116 ------------ 94 -----------
117 95
118 Fasta file 96 Fasta file
119 PED file conversion 97 PED file conversion
120 98
121 --------------------------------------------------- 99 ---------------------------------------------------
122 100
123 --------------- 101 ---------------
124 Working example 102 Working example
125 --------------- 103 ---------------
126 104
127 Input files 105 Input file
128 =========== 106 ==========
129 107
130 PED file 108 PED file
131 --------- 109 ---------
132 110
133 :: 111 ::
134 112
135 CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A 113 CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A
136 114
137 Parameters 115 Parameter
138 ========== 116 =========
139 117
140 Output name -> pedFile 118 Output name -> pedFile
141 119
142 Output files 120 Output file
143 ============ 121 ===========
144 122
145 pedFile.fa 123 pedFile.fa
146 ---------- 124 ----------
147 125
148 :: 126 ::
149 127
150 YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY 128 YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY
151 129 ]]></help>
152
153 </help>
154 130
155 <citations> 131 <citations>
156 <!-- [HELP] As DOI or BibTex entry --> 132 <!-- [HELP] As DOI or BibTex entry -->
157 <citation type="bibtex">@article{Dereeper03062015, 133 <citation type="bibtex">@article{Dereeper03062015,
158 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 134 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},